Oomph and Hawk
Oomph has a feature that synchronizes preferences across workspaces (see bug 490549).
This can be a problem if you expect different workspaces to have different Hawk indexes. If so, you should reconfigure Oomph so it does not record the /instance/org.eclipse.hawk.osgiserver
preferences node at the "User" and "Installation" levels.
To do this, go to "Window > Preferences", select "Oomph > Setup Tasks > Preference Recorder", check "Record into", select "User" and make sure /instance/org.eclipse.hawk.osgiserver/config
either does not appear or is unchecked. It should be the same for "Installation" and "Workspace".